Nanite Destruction: Omega vs Alpha
by VRmaster300
Summary: Circe is taken to Providence for treatment after "The Alliance", and stays there with Rex. The Omega-1 nanite isnt alone, Van Kliss made his own prototype that he stashed away, lying dormant till it carryed out its main objective...


**I do not own Generator Rex or any factors of the franchise. **

**A/N: I was watching last night's episode of Back in Black as well as another show and ideas start kicking into my mind about a possible plot for my own Generator Rex fic. **

**This is a test sample/prologue for it, I will start using a bit of ideas from the second season and wait as the third season starts up with more episodes.**

**This fic starts off just a little bit before the episode Mixed Signals.**

**In this fic Circe ended up waking up a little later after the events of the bug jar in The Alliance, and joins Providence, not as a full agent, but to be close to Rex as she has no other place. Yes I know that she went his Rex's old gang in the show, but I wanted to keep her close to him.**

**At the moment I don't know if I will keep Cesar going bad guy as he is shown so far in the new season, but will decide that later. Though he will have a bit of a alternative hidden agenda in his first appearance of this fic.**

**Let me know what you all think.**

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><p>"<em>She's a freak"<em>

"_Kill her"_

"_Get away you monster"_

Circe bolted awake on her bed as she gasped for air.

Her nightmares were becoming worse every night.

The fears of her past were suddenly attempting to catch back up with her, and she wasn't willing to face them again.

"Snore…..pizza with pineapple and salmon,"

Circe looked to her side at the sleeping Rex who was snoring.

Even in his sleep he still thinks about fast food, she thought.

Circe wiped the sweat from her forehead and lay herself back down on the bed, snuggling closer to Rex in his sleep.

She began thinking back over how things had changed for her, the events that led to her now sleeping here next to Rex in his room at Providence.

She recalled how she had been hit to the head after she had turned on Van Kliss at the bug jar. Her head injury was more severe then she originally thought and she didn't regain consciousness. Rex had taken her back to Providence to receive medical attention since he didn't want to just go and leave her at a regular hospital where he knew that the medics wouldn't want to tend to her injuries because she was an EVO, so he had little choice but to take her back to Providence with him.

She laid her head down on his chest so that her ear was listening to his heartbeat, and sighed.

When she had awaken in the medical wing filled with Providence medics, she was about to go berserk and try to fight her way out, but all the other medics were told to step away and leave the girl by an older woman. Circe recognized her as someone Rex once called Dr Holiday. The doctor sat down to talk to her and told her about how Rex had saved her life by bringing her to Providence since her concussion would have been very dangerous if she hadn't received medical attention when she did.

As she listened to Rex's heartbeat she used one of her hands to feel upwards through her hair and where a scar was no her scalp.

She had had some minor surgery done afterwards, and all during her time lying down in that hospital bed she thought about how where she was suppose to go from here.

She couldn't go back to Van Kliss now, she had been on the run and living on the streets before she crossed paths with him, after she had run away from her foster home years ago.

"I'll take a pizza with…..pineapple…and salmon," Rex began saying in his sleep.

Circe laughed a bit before going back to her thoughts.

She wasn't sure how things had gone as they had after that, but it seemed the Rex had fought with the man called white knight about letting her stay at Providence since she had no where left to go.

From what the lady known as Holiday told her, White was against letting her stay saying that she was a rouge evo, and that Providence wasn't a foster home.

In the end Holiday told her that white decided to let her stay after another one of his solder's, the one called Six, that white had only agreed to let her stay so that she could be used to in one area that not most of Providence had, someone with a hold over Rex.

Circe chuckled at that thought, they all seemed to think that she could control Rex, just because of a crush he has one her.

Truth be told Circe did think she had a certain control over Rex due to his little crush on her, so they were right on a certain level.

She still wasn't fully sure of why she decided to stay at Providence, but at that moment she needed to be somewhere with someone who wasn't going to use her, or see her as an evo, and the only place like that was at Rex's side. And so she stayed.

She had a confusing interrogation by white knight, but thankfully that was most of the bad of staying there.

She wasn't required to go out and be a field operative like Rex, White only was keeping her around to give Rex a reason to stay aligned with Providence and hopefully try to straighten him out in some way.

Circe turned her head and looked over Rex's sleeping form to see a lab coat hanging on a chair on the other side of the room.

And even while not being forced to go onto the front lines, White said she wasn't going to stay around and do nothing either. Holiday had decided to use her as a assistant in the medical wing, so Circe was working under her for the time being.

She was not given much acknowledgment seeing as the majority of Providence knew she used to work for Van Kliss, so people were still uneasy around her.

Other then Rex the only other people who actually tried to make her feel like a normal person was Holiday, Six, and the monkey….

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><p><strong>In another part of Providence…<strong>

"Hey, I'm a chimp," yelled Bobo in his sleep."

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><p><strong>Back in Rex and Circe's room<strong>

Six acted neutral towards her, just seeing her as another part of Providence.

Bobo treated her no different than before.

Holiday though seemed to act almost as if she were trying to put on an older sister role to Circe, which confused Circe since she didn't understand why she was doing that.

Almost a month had gone by now since that day in the bug jar, and she was still trying to adjust to her new living conditions.

She had been having nightmares a lot for the last few weeks, and since Rex's room was right next to her own he had heard her tossing and turning in her sleep much often. On some occasions Rex would end up sneaking to her room to talk to her till she feel asleep, and on some others she had actually asked him to stay and sleep next to her to try to help her sleep past her nightmares.

In this time she was still unsure of what her relationship with Rex was.

He liked her, and she actually did in turn like him, he was the first person in a long time that would always refer to her as a human, not as an evo.

She wasn't sure if they were a couple, they still in all this time did not have a first kiss, or anything else other than a hug.

One thing that Circe noted was that Rex was not like most of the guys she had come across in her time.

When she had asked him to sleep next to her during her nightmares, that was exactly what he did, just sleep. He never even noted that she was barely dressed, only wearing a loose shirt and shorts that might as well count as underwear.

Rex had never once in these nights ever tried to take advantage of her, nor to ever try to put his arm around her while she slept, he actually respected her boundaries.

This was the first thing that made Circe think that maybe Rex didn't really think of her than more than just a friend.

In his sleeping state, Rex suddenly took his arm and wrapped it around Circe, she felt the pressure of his arm on her waist and instead of pushing it back accepted it.

But she wasn't giving up just quickly like that; she recalled how Holiday told her how Rex would sometimes constantly say that Circe herself was something he would have on his mind a lot.

She let herself ease into Rex's hold as she tried to go back to sleep, hoping that her nightmares would go away for the rest of the night.

"Pizza…Pineapple…Salmon," Rex kept saying in his sleep as well as drooling a bit.

Circe sighed; Rex had some strange tastes in food.

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><p><strong>Providance Control room<strong>

"You're telling me that he's been sleeping in the same room as that girl for the last week, possibly more," said White as he talked through the communication channel with Six and Holiday.

"It would appear so," said Six.

"Why hasn't anyone done anything about this?" demanded White.

"Sir, with all respect they aren't doing anything inappropriate," said Holiday.

"How are you so sure?" said White.

"I've put certain sensors and body temperature reading equipment in her room when we gave it to her. Her readings show that her body has been creating internal chemicals that relate to nightmares, and during his time in her room her levels have dropped. He seems to be keeping her levels normal by providing her nearby support while she sleeps," said Holiday.

"I don't care about that, I let that girl stay so that she could help in controlling Rex, not to….."

"White, while I agree that this type of action isn't right, as long as they aren't engaging in "other" kind of involvement, I don't think it's a major issue. Like you said, you want her here to try to have some control over Rex, and she needs him to try to feel normal, just as Rex desires as well," said Six.

White was not happy, but Six was making a point.

"If there are consequences from this later on, know that it will be on your heads," said White as the screen went black, indicating that he cut off the communication.

Holiday sighed, and Six just turned to her and said, "Despite what I told White, something still has to be done."

Holiday stared at him, "What do you suggest we do?"

"I'll take Rex, you take Circe. We'll have to give each of them "the talk"," said Six.

"WHAT? I only ever did that with my sister before she turned Evo," said Holiday.

"Sometimes these things have to be done, you think I want to have "the talk" with Rex," said Six.

Holiday laughed and turned to leave, "Good luck Six."

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><p><strong>Somewhere else in the mountains<strong>

A strange tube shaped craft exited out of a time warp and slowed down and its occupant, Cesar Salazar, started observing his screens.

"That was close; I thought I was a goner for a second there,"

Warning, Beacon from Omege-1 nanite detected,

Cesar stopped his current analysis of his ship and started locking onto the beacon from the O-1.

Warning, Beacon from Alpha-0 nanite detected.

"What, the Alpha zero, but that's not suppose to exist," said Cesar in shock.

He quickly began altering his ship's systems to start homing in on the two beacons.

He opened a file in his system, and a screen came up.

_**Code name: Alpha-0 nanite**_

_**Function: Unknown**_

_**Creator: Van Kliss**_

_**Status: Unknown**_

_**Classification: Terminate on site no matter what.**_

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><p><strong>Do not know when the next chapter will be out, as I have some school work to catch up on, as well as need to rewatch a couple of episodes of the series.<strong>

**For those who are reading my pokemon fic, The Wrong Spell, I had the next chapter ready but it got deleted after a computer error, so I will have to rewrite it, thought it may be a shorter version then from what I originally planned. Maybe tomorrow, or next week, depending on what time I have.**

**Read & Review.**


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